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At least 793 records · Page 44Linked to original sources
PubMed1999

Mapping of human WHN gene in a 17q11.2 YAC contig and identification of an intragenic STR.

The recently isolated human WHN gene has been previously assigned to chromosome 17q11-12 using radiation hybrids. In this study, we constructed a YAC contig covering 17q11.2 between crystallinBA1 and neurofibromatosis 1 genes. By ordering known and novel markers, we determined the position of the WHN gene, and of the closely linked retinal 4 and sodium/dicarboxylate cotransporter genes. We also identified a new mononucleotide polymorphism contained within the untranslated exon 1 of the WHN gene, which may be useful for linkage and LOH studies.

Chromosomes, Artificial, Yeast↗
PubMed1995

Mapping dystrophin gene recombinants in Greek DMD/BMD families: low recombination frequencies in the STR region.

A systematic study of 42 Greek DMD/BMD families using 14 polymorphic markers that span the dystrophin gene was performed in order to assess the position and frequency of recombinants in the Greek population and to test whether "hot spots" of recombination and deletions coincide when exclusively studying DMD/BMD families. We report a low percentage of recombination between markers STR44 and STR50; otherwise, the distribution of recombination events in other parts of the gene is largely in agreement with previously published data on Centre d'Etude du Polymorphisme Humaine families. We therefore propose that recombination frequencies and the correlation between recombination and deletion "hot spots" should be evaluated on DMD/BMD families exclusively.

Chromosome Mapping↗
PubMed1995

Developmental and pathogen-induced activation of an msr gene, str 246C, from tobacco involves multiple regulatory elements.

A family of genes, the so-called msr genes (multiple stimulus response), has recently been identified on the basis of sequence homology in various plant species. Members of this gene family are thought to be regulated by a number of environmental or developmental stimuli, although it is not known whether any one member responds more specifically to one stimulus, or whether each gene member responds to various environmental stimuli. In this report, we address this question by studying the tobacco msr gene str246C. Using transgenic tobacco plants containing 2.1 kb of 5' flanking DNA sequence from the str246C gene fused to the beta-glucuronidase (GUS) coding region, the complex expression pattern of the str246C promoter has been characterized. Expression of the str246C promoter is strongly and rapidly induced by bacterial, fungal and viral infection and this induction is systemic. Elicitor preparations from phytopathogenic bacteria and fungi activate the str246C promoter to high levels, as do wounding, the application of auxin, auxin and cytokinin, salicylic acid or copper sulfate, indicating the absence of gene specialization within the msr gene family, at least for str246C. In addition, GUS activity was visualized histochemically in root meristematic tissues of tobacco seedlings and is restricted to roots and sepals of mature plants. Finally, analysis of a series of 5' deletions of the str246C promoter-GUS gene fusion in transgenic tobacco plants confirms the involvement of multiple regulatory elements. A region of 83 bp was found to be necessary for induction of promoter activity in response to Pseudomonas solanacearum, while auxin inducibility and root expression are apparently not controlled by this element, since its removal does not abolish either response. An element of the promoter with a negative effect on promoter activation by P. solanacearum was also identified.

Base Sequence↗
PubMed1995

Refined mapping of caltractin in human Xq28 and in the homologous region of the mouse X chromosome places the gene within the bare patches (Bpa) and striated (Str) critical regions.

Caltractin belongs to a family of calcium-binding proteins and is a structural component of the centrosome. A human caltractin cDNA (CALT) has recently been mapped by fluorescence in situ hybridization (FISH) to Xq28. We report here refined mapping of the human CALT gene and its murine homolog between the loci DXS1104 (DXHXS1104) DXS52 (DXHXS52) by PCR and Southern analysis on YACs and somatic cell hybrids from the region in both species. These mapping studies place the gene within the critical region for the murine X-linked dominant, male lethal mutations bare batches and striated.

Animals↗
PubMed1995

Population study of 3 STR loci in the Basque Country (northern Spain).

The tetrameric STRs, HUMTH01, HUMVWA31A and HUMFES/FPS, were studied in a population from the Basque Country (northern Spain) for their frequency distribution and applicability to identity and paternity testing. All systems conformed to Hardy-Weinberg equilibrium; pairwise comparisons demonstrated the allelic independence between loci, and furthermore, all systems seemed to be in agreement with expectations from the Stepwise Mutation Model (SMM) of the mutation-drift theory, which indicates the homogeneity of the population and suggests a replication slippage mechanism as a possible model for generating alleles. A comparison with other population groups appeared to indicate that frequencies are well conserved in Caucasians, but differ from other racial groups. The calculated parameters "a priori probability of exclusion" (PEX) and "index of discrimination" (ID), show the informativeness of these loci for the determination of identity and relatedness of individuals.

Alleles↗
PubMed1996

Analysis of the STR loci HUMF13A01, HUMFXIIIB, HUMLIPOL, HUMTH01, HUMTPOX and HUMVWFA31 in a Japanese population.

Population studies on six short tandem repeat loci, HUMF13A01, HUMFXIIIB, HUMLIPOL, HUMTH01, HUMTPOX and HUMVWFA31 were carried out in a sample of unrelated Japanese individuals (n = 337-545) living in Gifu Prefecture (central region of Japan). Five alleles could be identified for HUMFXIIIB, six for HUMF13A01, HUMLIPOL, HUMTH01 and HUMTPOX, and eight for HUMVWFA31. For all/six loci no deviations from the Hardy-Weinberg equilibrium hypothesis were detected. The mean exclusion chance ranged from 0.22 to 0.60, the power of discrimination from 0.63 to 0.93, and the expected heterozygosity from 0.43 to 0.80. Allele frequency distributions for the loci in the Japanese sample were not similar to those in samples from other racial or ethnic groups except for the Chinese (for HUMTPOX). The results demonstrate that HUMTH01, HUMTPOX and HUMVWFA31 are more useful for forensic investigations in the Japanese population that the other three loci.

Alleles↗
PubMed1996

Analysis of STR-PCR products with high-resolution denaturing PAGE.

The Pharmacia Multiphor II horizontal electrophoresis chamber is a widespread tool for analysis of PCR products in forensic casework. Up to date, however, there is no protocol for successfully running high-resolution denaturing PAGE (poly-acrylamide gel electrophoresis) on a horizontal electrophoresis chamber. We modified the electrophoresis conditions to make this possible.

DNA↗
PubMed1995

Validation of the STR system FES/FPS for forensic purposes in an Austrian population sample.

The short tandem repeat system FES/FPS was amplified by the polymerase chain reaction (PCR) in 211 unrelated Austrians and analysed by horizontal, non-denaturing electrophoresis. The allele distribution was in Hardy-Weinberg equilibrium. No mutations were found in 25 families (50 meioses). The mean exclusion chance was 0.49, the discriminating power 0.86 and the heterozygosity rate 74.4%. Amplification could be achieved with as little as 100 pg of high molecular weight DNA, which could be reduced to 75 pg by using 32 instead of 30 cycles. By reamplifying 1 microliter for another 15 cycles, the threshold could be reduced to less than 20 pg. In a degradation experiment DNA extracted from bloodstains stored for up to 24 days in a moist chamber and DNA boiled for up to 18 min could be amplified.

Austria↗
PubMed1995

Short tandem repeat (STR) system HumD21S11: population genetic study on an Italian population.

Allele frequencies of the Short Tandem Repeat locus HumD21S11 were determined analysing 119 unrelated individuals from the area of Milano (Northern Italy). A total of 13 alleles was detected. One allele (< 26) was found which has never been observed in a wider German population sample. The system showed neither significant deviation from Hardy-Weinberg equilibrium nor significant differences with a German population sample.

Gene Frequency↗
PubMed1996

The str gene cluster for the biosynthesis of 5'-hydroxystreptomycin in Streptomyces glaucescens GLA.0 (ETH 22794): new operons and evidence for pathway-specific regulation by StrR.

Two divergently oriented operons, strXU and strVW, located within the gene cluster for 5'-hydroxystreptomycin (5'-OH-Sm) biosynthesis in Streptomyces glaucescens strain GAL.0 (ETH 22794), were analysed by DNA sequencing and transcription/regulation studies. Three genes, strU and strVW, are conserved in a similar arrangement but in a different location within the str/sts gene cluster of the Sm-producing strain S. griseus N2-3-11. The four putative products resemble NDP-4-ketohexose 3,5-epimerases (StrX, M(r) 20.2 kDa), NAD(P)-dependent oxidoreductases (StrU, 45.6 kDa), and ABC-transporters (StrV, 61.8 kDa; StrW, 63.4 kDa). These genes are apparently involved in the biosynthesis of 5'-OH-Sm because the promoters of both operons are activated in trans by the activator StrR of S. griseus N2-3-11, when cloned in S. lividans 66 TK23. A sequence motif resembling the consensus sequence GTTCGActG(N)11CagTcGAAc for binding of StrR was identified within the intergenic region of strX and strV. Specific binding of StrR to this site was demonstrated by gel retardation assays using purified His*Tag-StrR.

ATP-Binding Cassette Transporters↗
PubMed2000

Further sequence and length variation at the STR loci HumFES/FPS, HumVWA, HumFGA and D12S391.

This paper reports population data and statistics for the HumFES/FPS, HumVWA, HumFGA and D12S391 loci in Austria. The sequences of some rare and new variant alleles which have been identified in the course of the present population study and other investigations are described. Sequence variation occurred in a HumFES/FPS allele revealing an (ATTT)9 structure and an A to C transversion in the 5' flanking region. At the HumVWA locus the structural type of the common allele 14 has been found in one allele 13 and in three examples of allele 15. Additionally the TCTA (TCTG)3(TCTA)n structure has been observed in three examples of allele 13 and one allele 14, which is very uncommon. Another allele 14 showed a C to T transition in the third of nine TCTA repeats. The sequences of three length variations at the HumFGA locus, namely the alleles 16, 19.2 and 21.2 are reported. At the D12S391 locus a novel 19.1 allele was found in this study. An extended nomenclature is proposed for the HumVWA locus to denominate sequence variants in a precise but simple way.

Chromosome Mapping↗
PubMed2002

Purification of STR-multiplex-amplified microsamples can enhance signal intensity in capillary electrophoresis.

In this study, the effect of sample purification on total signal intensities of samples amplified with genRES MPX-2 (nine-locus multiplex) prior to capillary electrophoretic analysis has been investigated. Sample purification with the Qiaquick PCR purification kit led to an increase of the relative fluorescent signal intensity by a factor of 3.8 +/- 0.8. In contrast, the application of larger sample volumes led to a decrease of signal intensities from 20% to 80%, depending on whether the samples were purified or not. In addition, increase of injection time showed a linear increase of signal intensity between 3 s and 10 s. Increasing the number of PCR cycles from 30 to 33 also led to a significant increase of signal intensities. Nevertheless, this increase greatly depended on the fragment lengths and was sometimes accompanied by the appearance of non-specific signals. In combination, optimisation of sample preparation and increase of injection time may intensify signals up to 12-fold, thereby increasing the overall sensitivity of the assay. This may be of special interest for forensic analysis of microspecimens containing limited amounts of DNA.

DNA↗
PubMed2002

Allele frequency data for 16 STR loci in the Vietnamese population.

The short tandem repeat systems ACTBP2, D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, VWA, D8S1179, TPOX and FGA were studied in a population sample from Vietnam (178 individuals, mainly from the Hanoi area). The 16 loci met Hardy-Weinberg expectations and possess a combined power of discrimination greater than 0.9999999999999999998 and a combined power of exclusion greater than 0.99999994 in this Vietnamese population.

Alleles↗
PubMed2003

Variation at 16 STR loci in Rwandans (Hutu) and implications on profile frequency estimation in Bantu-speakers.

A data set of 16 autosomal STRs (the 13 CODIS loci plus HumCD4, HumFES, HumF13A1) was obtained in a sample of 52 unrelated Hutus from Rwanda. Genotypes at all loci met Hardy-Weinberg expectations with the exception of HumCSF1PO. No significant evidence of association across alleles at independent loci was obtained. Statistical parameters demonstrated the forensic usefulness of the analysed systems (combined PE=0.9999996, combined PD=1:2.27 x 10(18)). Pairwise comparisons showed that the Hutu gene pool differs substantially from that of other Bantu-speaking populations suggesting the use of ethnic-specific population databases in forensic casework analysis. The introduction of a non-negligible bias was confirmed by calculating the differences between multiple-locus profile frequencies of western and eastern Bantoids using local and non-local reference databases.

Alleles↗
PubMed2003

New sensitive amplification primers for the STR locus D2S1338 for degraded casework DNA.

PCR primers for the locus D2S1338 were redesigned in order to reduce the length of the amplification product compared with the conventional design. The new amplification primers were applied to highly degraded casework samples, which gave no or only weak results for D2 in previous analyses. The application of the new primers resulted in an increased overall typing success rate. In a concordance study between the conventional and the newly designed primers, no genotype differences were revealed in 503 randomly selected individuals. This suggests robust amplification conditions with respect to mutation-based allele drop-out.

DNA Fingerprinting↗